STAVAG is a method that identify directionally variable genes (DVGs) and temporally variable genes (TVGs) from spatial transcriptomics (ST) data. It is a unified gradient-boosting framework that models spatial-temporal information to uncover biological meaningful DVGs and TVGs.
For detailed usage, please refer to STAVAG-Documentation.
It is recommended to use a Python version 3.9.
- set up conda environment for STAVAG:
conda create -n STAVAG python==3.9
- activate STAVAG from shell:
conda activate STAVAG
- you can install the important Python packages used to run the model are as follows:
pip install scanpy[leiden]
pip install lightgbm
pip install numpy
pip install matplotlib
pip install scikit-learn
pip install scipy
- now you can install the STAVAG Python package as follows:
pip install STAVAG